Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006371.1 Kokia drynarioides strain JFW-HI SEQ_120947, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 908
Length: 1514
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Found at i:392 original size:175 final size:175
Alignment explanation
Indices: 1--1514 Score: 2120
Period size: 175 Copynumber: 8.7 Consensus size: 175
* * *
1 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
** * * **
66 TCTTCATAAAACATTCCATGTCAATAAAATGTCTGCATACCAATCTCTTCGCAAACAAATGTTCA
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
*
131 AAAA-AAAACATCGCCACCCA-CGAAGTGGTCAGGAAACAAATTCC
131 AAAAGAAAACATCGCCACCCAGC-AAGTGGCCAGGAAACAAATTCC
* ** * *
175 TAACATAGTAAGAAGCAAATATGATAATACAACAAGCCACTAAATAACTAATCATTTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
* * * * *
240 TCTTCATGAAACATTCTGTGTCAATAAAATGCCAGTATACCAATCGCTTCACGGACAAATGTTCA
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
* *
305 AAAAGAAAACATTGCCACCCAGCAAGTGGCCAAGAAACAAATTCC
131 AAAAGAAAACATCGCCACCCAGCAAGTGGCCAGGAAACAAATTCC
*
350 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
* * *
415 TCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATCGCTTCGCAGACAAATGTTC-
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
* * * * * * *
479 AAAAGAAAACATTGTCAACCAACAAGCGGGCAGGAAACAAATTTC
131 AAAAGAAAACATCGCCACCCAGCAAGTGGCCAGGAAACAAATTCC
*
524 TAACATAGTAAGAAGCAAATATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
* * * * * * ** *
589 TCTTCATCAAATATTTTGTGTAAATATAATGTTGGCATACCAATCATTTTGCGGACAAATGTTCA
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
* * *
654 AAAAGAAAACATCGCCAGCCACCAAGTGGGCAGGAAACAAATTCC
131 AAAAGAAAACATCGCCACCCAGCAAGTGGCCAGGAAACAAATTCC
* *
699 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCATCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
* * * *
764 TCTTCACAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATTGCTTCGCGAACAAATGTTCA
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
* * * * **
829 AAAAGAAAACATTGTCAACAAGCAAGTGGGTAGGAAACAAATTCC
131 AAAAGAAAACATCGCCACCCAGCAAGTGGCCAGGAAACAAATTCC
* * * *
874 TAACATAGTAAGAAGCAAATATGATAATACGACAAACCACTAAATAATTAATCATTTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
* * * *
939 TC-TCATGAAACATTATGTGTCAATAAAATGTCGGCATACCAATCGCTTCACGGGCAAATGTTCA
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
* *
1003 AAAAGAAAACATCGCCACCCACCAAGTGGCCAGGAAACAAATTCA
131 AAAAGAAAACATCGCCACCCAGCAAGTGGCCAGGAAACAAATTCC
* * *
1048 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
** * * * **
1113 TCTTCATAAAACATTCCATGTCAATAAAATGTCTGCATACCAATCTCTTTGCAAACAAATGTTCA
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
* * * * *
1178 AAAAAAAAACATCGTCATCCA-CGAAGTGGCTAGGAAACAAATTTC
131 AAAAGAAAACATCGCCACCCAGC-AAGTGGCCAGGAAACAAATTCC
* * * *
1223 TAACATAGTAAGAAGCAAATATGATAAAACGACAAGCCACTAAATAATTAATCATTTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
* * *
1288 TCTTCATGAAACATTCTGTGTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCA
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
* *
1353 AAAAGAAAACATCGCCACCGAGCAAGTGGCCAAGAAACAAATTCC
131 AAAAGAAAACATCGCCACCCAGCAAGTGGCCAGGAAACAAATTCC
*
1398 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
* *
1463 TCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATCGCTTCGC
66 TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGC
Statistics
Matches: 1174, Mismatches: 160, Indels: 11
0.87 0.12 0.01
Matches are distributed among these distances:
174 423 0.36
175 749 0.64
176 2 0.00
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (175 bp):
TAACATAGTAAGAAGCAAACATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
TCTTCATAAAACATTCTGTGTCAATAAAATGTCGGCATACCAATCGCTTCGCGGACAAATGTTCA
AAAAGAAAACATCGCCACCCAGCAAGTGGCCAGGAAACAAATTCC
Found at i:646 original size:349 final size:351
Alignment explanation
Indices: 1--1514 Score: 2348
Period size: 349 Copynumber: 4.3 Consensus size: 351
* * * *
1 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
* *
66 TCTTCATAAAACATTC-CATGTCAATAAAATGTCTGCATACCAATCTCTTCGCAAACAAATGTTC
66 TCTTCATAAAACATTCTC-TGTCAATAAAATGTCGGCATACCAATCGCTTCGCAAACAAATGTTC
* * *
130 -AAAAAAAAACATCG-CCACCCACGAAGTGGTCAGGAAACAAATTCCTAACATAGTAAGAAGCAA
130 AAAAAAAAAACATCGTCAACCAACGAAGTGGGCAGGAAACAAATTCCTAACATAGTAAGAAGCAA
* *
193 ATATGATAATACAACAAGCCACTAAATAACTAATCATTTTCACCACATCTTCATGAAACATTCTG
195 ATATGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTG
* * *
258 TGTCAATAAAATGCCAGTATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATTGCCAC
260 TGTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATCGCCAC
*
323 CCAGCAAGTGGCCAAGAAACAAATTCC
325 CCACCAAGTGGCCAAGAAACAAATTCC
350 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
* *
415 TCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATCGCTTCGCAGACAAATGTTC-
66 TCTTCATAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATCGCTTCGCAAACAAATGTTCA
* * * *
479 AAAAGAAAACATTGTCAACCAAC-AAGCGGGCAGGAAACAAATTTCTAACATAGTAAGAAGCAAA
131 AAAAAAAAACATCGTCAACCAACGAAGTGGGCAGGAAACAAATTCCTAACATAGTAAGAAGCAAA
* * * * *
543 TATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACATCTTCATCAAATATTTTGT
196 TATGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTGT
* * ** ** ** *
608 GTAAATATAATGTTGGCATACCAATCATTTTGCGGACAAATGTTCAAAAAGAAAACATCGCCAGC
261 GTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATCGCCACC
* *
673 CACCAAGTGGGCAGGAAACAAATTCC
326 CACCAAGTGGCCAAGAAACAAATTCC
*
699 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCATCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
* * *
764 TCTTCACAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATTGCTTCGCGAACAAATGTTCA
66 TCTTCATAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATCGCTTCGCAAACAAATGTTCA
* * *
829 AAAAGAAAACATTGTCAA-CAA-GCAAGTGGGTAGGAAACAAATTCCTAACATAGTAAGAAGCAA
131 AAAAAAAAACATCGTCAACCAACG-AAGTGGGCAGGAAACAAATTCCTAACATAGTAAGAAGCAA
* *
892 ATATGATAATACGACAAACCACTAAATAATTAATCATTTTCACCACATC-TCATGAAACATTATG
195 ATATGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTG
* *
956 TGTCAATAAAATGTCGGCATACCAATCGCTTCACGGGCAAATGTTCAAAAAGAAAACATCGCCAC
260 TGTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATCGCCAC
* *
1021 CCACCAAGTGGCCAGGAAACAAATTCA
325 CCACCAAGTGGCCAAGAAACAAATTCC
* * * *
1048 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
* * *
1113 TCTTCATAAAACATTC-CATGTCAATAAAATGTCTGCATACCAATCTCTTTGCAAACAAATGTTC
66 TCTTCATAAAACATTCTC-TGTCAATAAAATGTCGGCATACCAATCGCTTCGCAAACAAATGTTC
* *
1177 AAAAAAAAAACATCGTCATCC-ACGAAGT-GGCTAGGAAACAAATTTCTAACATAGTAAGAAGCA
130 AAAAAAAAAACATCGTCAACCAACGAAGTGGGC-AGGAAACAAATTCCTAACATAGTAAGAAGCA
*
1240 AATATGATAAAACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCT
194 AATATGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCT
1305 GTGTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATCGCCA
259 GTGTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATCGCCA
* *
1370 CCGAGCAAGTGGCCAAGAAACAAATTCC
324 CCCACCAAGTGGCCAAGAAACAAATTCC
1398 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
*
1463 TCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATCGCTTCGC
66 TCTTCATAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATCGCTTCGC
Statistics
Matches: 1058, Mismatches: 96, Indels: 21
0.90 0.08 0.02
Matches are distributed among these distances:
348 3 0.00
349 737 0.70
350 317 0.30
351 1 0.00
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (351 bp):
TAACATAGTAAGAAGCAAACATGATAATATGACAAACCACTAAATAATTAATCAATTTCACCACA
TCTTCATAAAACATTCTCTGTCAATAAAATGTCGGCATACCAATCGCTTCGCAAACAAATGTTCA
AAAAAAAAACATCGTCAACCAACGAAGTGGGCAGGAAACAAATTCCTAACATAGTAAGAAGCAAA
TATGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTGT
GTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATCGCCACC
CACCAAGTGGCCAAGAAACAAATTCC
Found at i:1009 original size:524 final size:523
Alignment explanation
Indices: 1--1512 Score: 2377
Period size: 524 Copynumber: 2.9 Consensus size: 523
1 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
*
66 TCTTCATAAAACATTCCATGTCAATAAAATGTCTGCATACCAATCTCTTCGCAAACAAATGTTCA
66 TCTTCATAAAACATTCCATGTCAATAAAATGTCTGCATACCAATCTCTTTGCAAACAAATGTTCA
*
131 AAAAAAAACATCGCCACCCACGAAGTGGTCAGGAAACAAATTCCTAACATAGTAAGAAGCAAATA
131 AAAAAAAACATCGCCACCCACGAAGTGGGCAGGAAACAAATTCCTAACATAGTAAGAAGCAAATA
* *
196 TGATAATACAACAAGCCACTAAATAACTAATCATTTTCACCACATCTTCATGAAACATTCTGTGT
196 TGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTGTGT
* * *
261 CAATAAAATGCCAGTATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATTGCCACCCA
261 CAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATTGCCACCAA
326 GCAAGTGGCCAAGAAACAAATTCCTAACATAGTAAGAAGCAAACATGATAATATGACAAACCACT
326 GCAAGTGGCCAAGAAACAAATTCCTAACATAGTAAGAAGCAAACATGATAATATGACAAACCACT
391 AAATAATTAATCAATTTCACCACATCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATACC
391 AAATAATTAATCAATTTCACCACATCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATACC
* * * *
456 AATCGCTTCGCAGACAAATGTTCAAAAGAAAACATTGTCAACCAACAAGCGGGCAGGAAACAAAT
456 AATCGCTTCACAGACAAATGTTCAAAAGAAAACATCGCCAACCAACAAGCGGCCAGGAAACAAA-
521 TTC-
520 TTCA
* * * *
524 TAACATAGTAAGAAGCAAATATGATAATATGACAAGCCACTAAATAATTAATCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
* * *** * * **
589 TCTTCATCAAATATTTTGTGTAAATATAATGT-TGGCATACCAATCAT-TTTGCGGACAAATGTT
66 TCTTCATAAAACATTCCATGTCAATAAAATGTCT-GCATACCAATC-TCTTTGCAAACAAATGTT
* *
652 CAAAAAGAAAACATCGCCAGCCACCAAGTGGGCAGGAAACAAATTCCTAACATAGTAAGAAGCAA
129 CAAAAA-AAAACATCGCCACCCACGAAGTGGGCAGGAAACAAATTCCTAACATAGTAAGAAGCAA
* * * * * ** *
717 ACATGATAATATGACAAACCACTAAATAATTAATCAATTTCATCACATCTTCACAAAACATTCTC
193 ATATGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTG
* * * * * *
782 TGTCAATAAAATGTCGGCATACCAATTGCTTCGCGAACAAATGTTCAAAAAGAAAACATTGTCAA
258 TGTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATTGCCAC
** * * *
847 CAAGCAAGTGGGTAGGAAACAAATTCCTAACATAGTAAGAAGCAAATATGATAATACGACAAACC
323 CAAGCAAGTGGCCAAGAAACAAATTCCTAACATAGTAAGAAGCAAACATGATAATATGACAAACC
* * * * *
912 ACTAAATAATTAATCATTTTCACCACATC-TCATGAAACATTATGTGTCAATAAAATGTCGGCAT
388 ACTAAATAATTAATCAATTTCACCACATCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCAT
* * * * *
976 ACCAATCGCTTCACGGGCAAATGTTCAAAAAGAAAACATCGCCACCCACCAAGTGGCCAGGAAAC
453 ACCAATCGCTTCACAGACAAATGTTC-AAAAGAAAACATCGCCAACCAACAAGCGGCCAGGAAAC
1041 AAATTCA
517 AAATTCA
1048 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
1 TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
1113 TCTTCATAAAACATTCCATGTCAATAAAATGTCTGCATACCAATCTCTTTGCAAACAAATGTTCA
66 TCTTCATAAAACATTCCATGTCAATAAAATGTCTGCATACCAATCTCTTTGCAAACAAATGTTC-
* * *
1178 AAAAAAAAACATCGTCATCCACGAAGT-GGCTAGGAAACAAATTTCTAACATAGTAAGAAGCAAA
130 AAAAAAAAACATCGCCACCCACGAAGTGGGC-AGGAAACAAATTCCTAACATAGTAAGAAGCAAA
*
1242 TATGATAAAACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTGT
194 TATGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTGT
*
1307 GTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATCGCCACC
259 GTCAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATTGCCACC
*
1372 GAGCAAGTGGCCAAGAAACAAATTCCTAACATAGTAAGAAGCAAACATGATAATATGACAAACCA
324 AAGCAAGTGGCCAAGAAACAAATTCCTAACATAGTAAGAAGCAAACATGATAATATGACAAACCA
1437 CTAAATAATTAATCAATTTCACCACATCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATA
389 CTAAATAATTAATCAATTTCACCACATCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATA
1502 CCAATCGCTTC
454 CCAATCGCTTC
1513 GC
Statistics
Matches: 880, Mismatches: 99, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
522 1 0.00
523 177 0.20
524 653 0.74
525 49 0.06
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (523 bp):
TAACATAGTAAGAAGCAAACATGATAATATAACAAGCCACTGAATAATTAACCAATTTCACCACA
TCTTCATAAAACATTCCATGTCAATAAAATGTCTGCATACCAATCTCTTTGCAAACAAATGTTCA
AAAAAAAACATCGCCACCCACGAAGTGGGCAGGAAACAAATTCCTAACATAGTAAGAAGCAAATA
TGATAATACGACAAGCCACTAAATAATTAATCATTTTCACCACATCTTCATGAAACATTCTGTGT
CAATAAAATGCCGGCATACCAATCGCTTCACGGACAAATGTTCAAAAAGAAAACATTGCCACCAA
GCAAGTGGCCAAGAAACAAATTCCTAACATAGTAAGAAGCAAACATGATAATATGACAAACCACT
AAATAATTAATCAATTTCACCACATCTTTATAAAACATTCTCTGTCAATAAAATGTCGGCATACC
AATCGCTTCACAGACAAATGTTCAAAAGAAAACATCGCCAACCAACAAGCGGCCAGGAAACAAAT
TCA
Done.